def setUp(self): # self.t = LoadingTask() db = isotope_manager_factory().db lm = LoadingManager(db=db) # lm.irradiation = 'NM-251' # lm.level = 'H' self.t = LoadingTask(manager=lm)
def run(): hp = hpy() globalv.experiment_debug = True # t = ExperimentEditorTask() # p = os.path.join(paths.experiment_dir, 'demo.txt') # t._open_experiment(p) q = ExperimentQueue(delay_before_analyses=0, delay_between_analyses=0) q.automated_runs = [ AutomatedRunSpec(labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan'), AutomatedRunSpec(labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan'), AutomatedRunSpec(labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan'), AutomatedRunSpec(labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan'), AutomatedRunSpec(labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan') ] dbman = isotope_manager_factory() specman = SpectrometerManager() specman.load() ex = ExperimentExecutor( db=dbman.db, spectrometer_manager=specman, extraction_line_manager='', executable=True, ) ex.monitor = None ex.experiment_queues = [ q, ] ex.experiment_queue = q hp.setrelheap() t = ex.execute() t.join() # count_instances(group='sqlalchemy') return hp
def setUpClass(cls): cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff') cls.isotope_man.db.connect() expected_filtered_56954_01A = dict(Ar40bs_c=2.20831, Ar39bs_c=4.96090e-3, Ar38bs_c=0.0014621, Ar37bs_c=1.34848e-3, Ar36bs_c=7.40844e-3, Ar40bs=7.50865e-5, bs_fil=[44], Ar40_fil=[1, 9, 43], Ar39_fil=[11, 16], Ar40bl=0.0328504, #Ar39_Ar40=0.002255 Ar39_Ar40=1 / 443.1534341, Ar39_Ar40e=0.000023 ) expected_nonfiltered = dict(Ar40bs_c=2.20908914, Ar39bs_c=4.96081e-3, Ar38bs_c=0.0014706, Ar37bs_c=0.001349, Ar36bs_c=0.0074384, Ar40bs=7.50865e-5, bs_fil=[], Ar40_fil=[]) expected_filtered = dict( Ar40bs_c=0.159394, Ar40bs_ce=2.67938e-4, Ar39bs_c=1.58288e-2, Ar39bs_ce=7.9423e-5, Ar40bl_c=0.129651, Ar40bl_ce=0.003811, Ar40bl=0.031794, Ar40ble=0.0038013, Ar39_Ar40=0.1226, Ar39_Ar40e=0.0037, ar37df=3.348 ) cls.expected = expected_nonfiltered cls.expected = expected_filtered man = cls.isotope_man db = man.db with db.session_ctx(): ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff']) an = man.make_analysis(ans[4]) cls.analysis = an
def setUp(self): self.experimentor = Experimentor(connect=False, unique_executor_db=False) self.experimentor.db = db = isotope_manager_factory().db self._experiment_file = './data/experiment2.txt' self.exp_task = ExperimentEditorTask() self._load_queues()
def setUp(self): self.experimentor = Experimentor(connect=False, unique_executor_db=False ) self.experimentor.db = db = isotope_manager_factory().db self._experiment_file = './data/experiment2.txt' self.exp_task = ExperimentEditorTask() self._load_queues()
def setUpClass(cls): cls.isotope_man = isotope_manager_factory(name='pychrondata_dev') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db with db.session_ctx(): ans, tc = db.get_sample_analyses(['MB06-674', ], ['Minna Bluff']) an = man.make_analysis(ans[4]) cls._id=ans[4].id cls.analysis_no_pc = an
def setUpClass(cls): cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db with db.session_ctx(): ans, tc = db.get_sample_analyses(['AF-72', ], ['Minna Bluff']) cls.analyses=man.make_analyses(ans) cls.analysis = ans[0] cls.pkg=Packager()
def setUpClass(cls): cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db cls.sample_id = sid = 'AF-72' #cls.analysis_id = aid = string.ascii_uppercase.index('A') with db.session_ctx(): ans, tc = db.get_sample_analyses([sid, ], ['Minna Bluff']) cls.analyses = man.make_analyses(ans)
def setUpClass(cls): cls.isotope_man = isotope_manager_factory( name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db with db.session_ctx(): ans, tc = db.get_sample_analyses([ 'AF-72', ], ['Minna Bluff']) cls.analyses = man.make_analyses(ans) cls.analysis = ans[0] cls.pkg = Packager()
def setUpClass(cls): cls.isotope_man = isotope_manager_factory( name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db cls.sample_id = sid = 'AF-72' #cls.analysis_id = aid = string.ascii_uppercase.index('A') with db.session_ctx(): ans, tc = db.get_sample_analyses([ sid, ], ['Minna Bluff']) cls.analyses = man.make_analyses(ans)
def setUpClass(cls): cls.isotope_man = isotope_manager_factory(name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db cls.sample_id = sid = 'AF-72' cls.analysis_id = aid = string.ascii_uppercase.index('A') with db.session_ctx(): ans, tc = db.get_sample_analyses([sid, ], ['Minna Bluff']) an = man.make_analysis(ans[aid]) cls.analysis = an p = '../data/autoupdate_AF_72_1' cls.parser = AutoupdateParser() cls.parser.parse(p)
def setUpClass(cls): cls.isotope_man = isotope_manager_factory( name='pychrondata_minnabluff') cls.isotope_man.db.connect() man = cls.isotope_man db = man.db cls.sample_id = sid = 'AF-72' cls.analysis_id = aid = string.ascii_uppercase.index('A') with db.session_ctx(): ans, tc = db.get_sample_analyses([ sid, ], ['Minna Bluff']) an = man.make_analysis(ans[aid]) cls.analysis = an p = '../data/autoupdate_AF_72_1' cls.parser = AutoupdateParser() cls.parser.parse(p)
def setUp(self): db = isotope_manager_factory().db self.le = LabnumberEntry(db=db)
from pychron.core.helpers.logger_setup import logging_setup __author__ = 'ross' import unittest from pychron.core.ui import set_toolkit set_toolkit('qt4') from pychron.processing.autoupdate_parser import AutoupdateParser from test.database import isotope_manager_factory ISOTOPE_MANAGER = isotope_manager_factory(name='pychrondata_minnabluff') ISOTOPE_MANAGER.connect() SKIP_BLANKS = False, 'skip blanks' SKIP_SIGNALS = False, 'skip signals' SKIP_FITS = False, 'skip fits' logging_setup('arar_diff') class MassSpecPychronIsotopeTestCase(object): def setUp(self): pass def get_expected_value(self, k): p = self.parser
def run(): hp = hpy() globalv.experiment_debug = True # t = ExperimentEditorTask() # p = os.path.join(paths.experiment_dir, 'demo.txt') # t._open_experiment(p) q = ExperimentQueue(delay_before_analyses=0, delay_between_analyses=0) q.automated_runs = [ AutomatedRunSpec( labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan' ), AutomatedRunSpec( labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan' ), AutomatedRunSpec( labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan' ), AutomatedRunSpec( labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan' ), AutomatedRunSpec( labnumber='61312', duration=2.0, extraction_script='pause', measurement_script='air', mass_spectrometer='jan' ) ] dbman = isotope_manager_factory() specman = ArgusSpectrometerManager() specman.load() ex = ExperimentExecutor(db=dbman.db, spectrometer_manager=specman, extraction_line_manager='', executable=True, ) ex.monitor = None ex.experiment_queues = [q, ] ex.experiment_queue = q hp.setrelheap() t = ex.execute() t.join() # count_instances(group='sqlalchemy') return hp
import math import os from pychron.core.ui import set_toolkit set_toolkit('qt4') from pychron.processing.autoupdate_parser import AutoupdateParser from test.database import isotope_manager_factory isotope_man=isotope_manager_factory(name='pychron_dataset') isotope_man.db.connect(test=True) pp = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data', 'massspec_dataset_nofilter') # pp = '../data/massspec_dataset_nofilter' parser = AutoupdateParser() parser.parse(pp) msid='Unknown' sid='MB06-507' pid='Minna Bluff' class IntensityMixin(object): @classmethod def setUpClass(cls): aid=cls.analysis_id cls.sample_id = msid cls.analysis_id = aid db=isotope_man.db with db.session_ctx(): ans, tc = db.get_sample_analyses([sid, ], [pid])
def setUp(self): man = isotope_manager_factory() self.processor = Processor(bind=False, db=man.db)
#============= standard library imports ======================== #============= local library imports ========================== @profile def main(db): labn = db.get_labnumber('61311', # options='analyses' ) print '------------------------- got labnunmber' an = labn.analyses[0] print '------------------------- got analysis' a = IsotopeRecord(_dbrecord=an) load(a) print '------------------------- loaded' # @profile def load(a): a.load_isotopes() print '------------------------- isotopes loaded' a.calculate_age() if __name__ == '__main__': man = isotope_manager_factory() db = man.db db.connect() # db.sess.bind.echo = True main(db) #============= EOF =============================================
def setUp(self): man = isotope_manager_factory() self.processor = Processor(bind=False, db=man.db )
@profile def main(db): labn = db.get_labnumber('61311', # options='analyses' ) print '------------------------- got labnunmber' an = labn.analyses[0] print '------------------------- got analysis' a = IsotopeRecord(_dbrecord=an) load(a) print '------------------------- loaded' # @profile def load(a): a.load_isotopes() print '------------------------- isotopes loaded' a.calculate_age() if __name__ == '__main__': man = isotope_manager_factory() db = man.db db.connect() # db.sess.bind.echo = True main(db) #============= EOF =============================================
import math import os from pychron.core.ui import set_toolkit set_toolkit('qt4') from pychron.processing.autoupdate_parser import AutoupdateParser from test.database import isotope_manager_factory isotope_man = isotope_manager_factory(name='pychron_dataset') isotope_man.db.connect(test=True) pp = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'data', 'massspec_dataset_nofilter') # pp = '../data/massspec_dataset_nofilter' parser = AutoupdateParser() parser.parse(pp) msid = 'Unknown' sid = 'MB06-507' pid = 'Minna Bluff' class IntensityMixin(object): @classmethod def setUpClass(cls): aid = cls.analysis_id cls.sample_id = msid cls.analysis_id = aid db = isotope_man.db
def setUp(self): self.manager = isotope_manager_factory() self.manager.db.connect()